BioC 3.0: CHECK report for mQTL.NMR on perceval

Package: mQTL.NMR

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mQTL.NMR_1.0.0.tar.gz

StartedAt: 2015-04-10 04:06:00 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:11:30 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 329.5 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mQTL.NMR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mQTL.NMR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mQTL.NMR’ version ‘1.0.0’
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mQTL.NMR’ can be installed ... [3s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 loading without being on the library search path ... OK
* checking 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [224s/266s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
pre_mQTL         64.232  0.794  69.398
mQTL.NMR-package 62.887  0.989  75.627
align_mQTL       55.051  0.722  68.208
process_mGWA     10.342  0.068  11.362
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

* installing *source* package ‘mQTL.NMR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mQTL.NMR)

name	user	system	elapsed
SRV	2.744	0.066	4.820
SRV.plot	2.526	0.080	4.698
SRV_lod.plot	0.208	0.011	0.355
Top_SRV.plot	2.358	0.072	3.974
alignSp	1.343	0.031	2.500
align_mQTL	55.051	0.722	68.208
attachSegments	1.073	0.020	1.221
circle_mQTL	0.268	0.010	0.479
configureRSPA	0.023	0.007	0.081
format_mGWA	0.616	0.025	1.113
format_mQTL	1.219	0.039	2.403
load_datafiles	0.024	0.008	0.057
load_demo_data	0.001	0.001	0.001
mQTL.NMR-package	62.887	0.989	75.627
matchSegments	1.629	0.041	1.884
normalise	0.337	0.006	0.344
normalise_mQTL	3.489	0.089	3.708
peakPeaks	0.915	0.025	1.065
post_mQTL	0.479	0.058	0.660
ppersp	0.054	0.020	0.091
pplot	0.042	0.020	0.072
pre_mQTL	64.232	0.794	69.398
process_mGWA	10.342	0.068	11.362
process_mQTL	1.000	0.037	1.161
segmentateSp	1.378	0.042	1.467
selectRefSp	2.086	0.010	2.212
setupRSPA	0.023	0.008	0.031
sgolay	0.001	0.000	0.005
sgolayDeriv	0.420	0.001	0.432
simple.plot	2.561	0.054	3.048
summary_mQTL	0.057	0.008	0.067