cosmo 1.22.0
Oliver Bembom
| Snapshot Date: 2012-06-22 17:01:39 -0700 (Fri, 22 Jun 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/cosmo | | Last Changed Rev: 64678 / Revision: 66944 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/cosmo.Rcheck’
* using R version 2.15.0 (2012-03-30)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cosmo/DESCRIPTION’ ... OK
* this is package ‘cosmo’ version ‘1.22.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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 ... NOTE
File ‘cosmo/R/zzz.R’:
.onLoad calls:
require(methods)
.onAttach calls:
cat(paste("\nWelcome to cosmo version", packageDescription("cosmo")$Version, "\n\n"))
cat("cosmo is free for research purposes only. For more details, type\n")
cat("license.cosmo(). Type citation('cosmo') for details on how to cite\n")
cat("cosmo in publications.\n")
Package startup functions should not change the search path.
Package startup functions should use ‘packageStartupMessage’ to
generate messages.
See section ‘Good practice’ in ?.onAttach.
* 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 compiled code ... NOTE
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/cosmo.Rcheck/cosmo/libs/cosmo.so’:
Found ‘exit’, possibly from ‘exit’ (C)
Objects: ‘alloc.o’, ‘constraints.o’, ‘donlp2.o’, ‘eval.o’,
‘init.o’, ‘matLib.o’, ‘theta.o’, ‘user_eval.o’
Found ‘printf’, possibly from ‘printf’ (C)
Object: ‘donlp2.o’
Found ‘putchar’, possibly from ‘putchar’ (C)
Object: ‘donlp2.o’
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Object: ‘donlp2.o’
Found ‘stderr’, possibly from ‘stderr’ (C)
Objects: ‘back.o’, ‘constraints.o’, ‘estarts.o’, ‘fit.o’, ‘init.o’,
‘io.o’, ‘lstarts.o’, ‘optimize.o’, ‘precalc.o’, ‘rio.o’,
‘theta.o’
Found ‘stdout’, possibly from ‘stdout’ (C)
Objects: ‘donlp2.o’, ‘io.o’
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* 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
NOTE: There were 3 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/cosmo.Rcheck/00check.log’
for details.
* installing *source* package ‘cosmo’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c alloc.c -o alloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c back.c -o back.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c constraints.c -o constraints.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c cosmo.c -o cosmo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c cregistration.c -o cregistration.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c donlp2.c -o donlp2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c estarts.c -o estarts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c eval.c -o eval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c fit.c -o fit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c free.c -o free.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c lstarts.c -o lstarts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c matLib.c -o matLib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c newx.c -o newx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c optimize.c -o optimize.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c posterior.c -o posterior.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c precalc.c -o precalc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c rio.c -o rio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c theta.c -o theta.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c user_eval.c -o user_eval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -IINCLUDE -I/usr/local/include -fpic -g -O2 -c xml.c -o xml.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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 -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/cosmo.Rcheck/cosmo/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘cosmo.Rnw’
** testing if installed package can be loaded
Welcome to cosmo version 1.22.0
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)