Package: MEDIPS

Version: 1.6.0

Command: /home/hpages/test-puck5/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings MEDIPS_1.6.0.tar.gz

StartedAt: 2012-04-01 02:04:38 -0700 (Sun, 01 Apr 2012)

EndedAt: 2012-04-01 02:11:01 -0700 (Sun, 01 Apr 2012)

EllapsedTime: 382.3 seconds

RetCode: 0

Status:  OK

CheckDir: MEDIPS.Rcheck

Warnings: 0

* using log directory '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/MEDIPS.Rcheck'
* using R version 2.15.0 RC (2012-03-22 r58802)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEDIPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEDIPS' version '1.6.0'
* 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 'MEDIPS' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 47.8Mb
  sub-directories of 1Mb or more:
    extdata  47.0Mb
* 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* 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 was 1 note.
See
  '/loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/MEDIPS.Rcheck/00check.log'
for details.

* installing *source* package 'MEDIPS' ...
** libs
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c annotate.c -o annotate.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c calibration.c -o calibration.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c coupling.c -o coupling.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c profile.c -o profile.o
gcc -std=gnu99 -I/home/hpages/test-puck5/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c roiprofile.c -o roiprofile.o
gcc -std=gnu99 -shared -L/usr/local/lib -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -L/home/hpages/test-puck5/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/hpages/test-puck5/bbs-2.10-bioc/meat/MEDIPS.Rcheck/MEDIPS/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'MEDIPS.Rnw' 
** testing if installed package can be loaded

* DONE (MEDIPS)

name	user	system	elapsed
MEDIPS.CpGenrich	83.833	2.656	86.692
MEDIPS.annotate	0.032	0.000	0.035
MEDIPS.calibrationCurve	4.056	0.168	4.247
MEDIPS.couplingVector	3.292	0.124	3.436
MEDIPS.coverageAnalysis	6.189	0.068	6.275
MEDIPS.exportWIG	3.536	0.020	3.572
MEDIPS.genomeVector	2.104	0.008	2.137
MEDIPS.getPositions	1.756	0.004	1.775
MEDIPS.mergeFrames	0.004	0.000	0.005
MEDIPS.methylProfiling	5.733	0.040	5.793
MEDIPS.normalize	3.620	0.032	3.667
MEDIPS.plotCalibrationPlot	6.288	0.044	6.350
MEDIPS.plotCoverage	7.421	0.020	7.459
MEDIPS.plotSaturation	34.614	0.036	34.680
MEDIPS.readAlignedSequences	1.764	0.028	1.806
MEDIPS.saturationAnalysis	31.790	0.048	31.874
MEDIPS.selectSignificants	79.225	0.620	79.978
MEDIPSset-class	0.000	0.000	0.001