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Package 110/467HostnameOS / ArchBUILDCHECKBUILD BIN
cosmo 1.18.0
Oliver Bembom
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/cosmo
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: cosmo
Version: 1.18.0
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings cosmo_1.18.0.tar.gz
StartedAt: 2011-10-20 12:23:14 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 12:23:56 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 41.6 seconds
RetCode: 0
Status:  OK 
CheckDir: cosmo.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/cosmo.Rcheck’
* using R version 2.13.2 (2011-09-30)
* 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 ‘1.18.0’
* checking package namespace 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 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 ... 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 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

cosmo.Rcheck/00install.out:

* installing *source* package ‘cosmo’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c alloc.c -o alloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c back.c -o back.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c constraints.c -o constraints.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c cosmo.c -o cosmo.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c cregistration.c -o cregistration.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c donlp2.c -o donlp2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c estarts.c -o estarts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c eval.c -o eval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c fit.c -o fit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c free.c -o free.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c init.c -o init.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c lstarts.c -o lstarts.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c matLib.c -o matLib.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c newx.c -o newx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c optimize.c -o optimize.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c posterior.c -o posterior.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c precalc.c -o precalc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c rio.c -o rio.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c theta.c -o theta.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -IINCLUDE -I/usr/local/include    -fpic  -g -O2 -c user_eval.c -o user_eval.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.8-bioc/R/include -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-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/cosmo.Rcheck/cosmo/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

Welcome to cosmo version 1.18.0 

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)

cosmo.Rcheck/cosmo-Ex.timings:

nameusersystemelapsed
addCon0.0240.0040.027
bfile2tmat0.0040.0000.006
bgModel0.0120.0040.015
boundCon-class0.0040.0040.004
cosmo0.9400.0040.946
license.cosmo0.0000.0040.004
makeBoundCon0.0000.0000.001
makeConSet0.0120.0000.011
makePalCon0.0000.0000.001
makePosFreqCon0.0000.0000.001
makeShapeCon0.0000.0000.002
makeShapeDiffCon0.0040.0000.003
makeSubMotifCon0.0000.0000.001
motifPWM0.0200.0000.018
palCon-class0.0080.0000.009
posFreqCon-class0.0120.0000.012
readConFile0.0640.0000.065
rseq0.2160.0000.212
shapeCon-class0.0000.0000.002
shapeDiffCon-class0.0040.0000.002
simScore0.8000.0000.803
subMotifCon-class0.0000.0000.001
transMats0.0040.0000.010
writeConFile0.020.000.03