BioC 3.0: CHECK report for mQTL.NMR on zin1

Package: mQTL.NMR

Version: 1.0.0

Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.0.0.tar.gz

StartedAt: 2015-04-10 02:19:30 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:22:59 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 209.0 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (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 ... [2s/3s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [150s/178s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 44.526  0.048  52.281
pre_mQTL         42.118  0.032  49.603
align_mQTL       39.698  0.080  50.382
process_mGWA      5.153  0.016   5.201
* 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	1.680	0.024	2.851
SRV.plot	1.732	0.012	2.248
SRV_lod.plot	0.140	0.000	0.138
Top_SRV.plot	1.576	0.012	1.960
alignSp	0.852	0.032	1.048
align_mQTL	39.698	0.080	50.382
attachSegments	0.732	0.004	0.828
circle_mQTL	0.204	0.004	0.360
configureRSPA	0.000	0.024	0.023
format_mGWA	0.529	0.004	0.827
format_mQTL	0.932	0.008	0.983
load_datafiles	0.020	0.004	0.024
load_demo_data	0.000	0.000	0.001
mQTL.NMR-package	44.526	0.048	52.281
matchSegments	0.692	0.004	0.700
normalise	0.288	0.000	0.290
normalise_mQTL	1.977	0.012	1.992
peakPeaks	0.356	0.004	0.363
post_mQTL	0.244	0.008	0.256
ppersp	0.056	0.004	0.062
pplot	0.036	0.000	0.039
pre_mQTL	42.118	0.032	49.603
process_mGWA	5.153	0.016	5.201
process_mQTL	1.04	0.02	1.06
segmentateSp	0.644	0.004	0.647
selectRefSp	1.376	0.000	1.378
setupRSPA	0.008	0.016	0.023
sgolay	0.004	0.000	0.002
sgolayDeriv	0.232	0.000	0.234
simple.plot	1.208	0.012	1.222
summary_mQTL	0.024	0.008	0.031