cosmo 1.19.0
Oliver Bembom
| Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/cosmo | | Last Changed Rev: 54802 / Revision: 55359 | | Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/cosmo.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cosmo/DESCRIPTION’ ... OK
* this is package ‘cosmo’ version ‘1.19.0’
* 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 installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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 ... 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
prepare_Rd: bgModel.Rd:49: Dropping empty section \references
prepare_Rd: boundCon-class.Rd:30: Dropping empty section \references
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
prepare_Rd: cosmo-class.Rd:58: Dropping empty section \references
prepare_Rd: cosmo-class.Rd:63-64: Dropping empty section \seealso
prepare_Rd: cosmo-class.Rd:65-66: Dropping empty section \examples
prepare_Rd: cosmo.Rd:142-144: Dropping empty section \details
prepare_Rd: cosmo.Rd:153: Dropping empty section \note
prepare_Rd: intInfo-class.Rd:88: Dropping empty section \note
prepare_Rd: intInfo-class.Rd:84: Dropping empty section \references
prepare_Rd: intInfo-class.Rd:92-93: Dropping empty section \examples
prepare_Rd: license.cosmo.Rd:10-11: Dropping empty section \arguments
prepare_Rd: license.cosmo.Rd:12-13: Dropping empty section \details
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
prepare_Rd: postProbs-class.Rd:36: Dropping empty section \references
prepare_Rd: postProbs-class.Rd:42-43: Dropping empty section \seealso
prepare_Rd: postProbs-class.Rd:44-45: Dropping empty section \examples
prepare_Rd: readConFile.Rd:15-16: Dropping empty section \details
prepare_Rd: rseq.Rd:35-37: Dropping empty section \details
prepare_Rd: rseq.Rd:51: Dropping empty section \note
prepare_Rd: rseq.Rd:49: Dropping empty section \references
prepare_Rd: rseq.Rd:53: Dropping empty section \seealso
prepare_Rd: shapeCon-class.Rd:42: Dropping empty section \references
prepare_Rd: shapeDiffCon-class.Rd:35: Dropping empty section \references
prepare_Rd: simScore.Rd:17-18: Dropping empty section \details
prepare_Rd: simScore.Rd:28: Dropping empty section \note
prepare_Rd: simScore.Rd:26: Dropping empty section \references
prepare_Rd: subMotifCon-class.Rd:33-34: Dropping empty section \note
prepare_Rd: subMotifCon-class.Rd:29: Dropping empty section \references
prepare_Rd: transMats.Rd:17-18: Dropping empty section \details
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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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) and $(LAPACK_LIBS) ... OK
* checking sizes of PDF files under ‘inst/doc’ ... NOTE
‘qpdf’ made some significant size reductions:
compacted ‘cosmo.pdf’ from 882Kb to 442Kb
consider running tools::compactPDF() on these files
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘cosmo’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c alloc.c -o alloc.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c back.c -o back.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c constraints.c -o constraints.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c cosmo.c -o cosmo.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c cregistration.c -o cregistration.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c donlp2.c -o donlp2.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c estarts.c -o estarts.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c eval.c -o eval.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c fit.c -o fit.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c free.c -o free.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c init.c -o init.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c io.c -o io.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c lstarts.c -o lstarts.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c matLib.c -o matLib.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c newx.c -o newx.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c optimize.c -o optimize.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c posterior.c -o posterior.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c precalc.c -o precalc.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c rio.c -o rio.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c theta.c -o theta.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c user_eval.c -o user_eval.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -IINCLUDE -I/usr/local/include -fPIC -g -O2 -c xml.c -o xml.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 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
installing to /Users/biocbuild/bbs-2.9-bioc/meat/cosmo.Rcheck/cosmo/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Loading required package: grid
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘cosmo.Rnw’
** testing if installed package can be loaded
Welcome to cosmo version 1.19.0
cosmo is free for research purposes only. For more details, type
license.cosmo(). Type citation('cosmo') for details on how to cite
cosmo in publications.
* DONE (cosmo)