BioC 3.0: CHECK report for mQTL.NMR on oaxaca

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 01:35:04 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 01:39:58 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 294.6 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch mQTL.NMR_1.0.0.tar.gz
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* 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-darwin13.4.0 (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/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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [198s/246s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 57.808  0.451  66.649
pre_mQTL         54.306  0.367  61.441
align_mQTL       50.638  0.382  70.280
process_mGWA      6.098  0.036   6.188
SRV.plot          2.903  0.042   5.207
* 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	2.516	0.048	4.993
SRV.plot	2.903	0.042	5.207
SRV_lod.plot	0.156	0.007	0.166
Top_SRV.plot	2.826	0.039	3.839
alignSp	1.386	0.022	2.743
align_mQTL	50.638	0.382	70.280
attachSegments	1.288	0.018	2.563
circle_mQTL	0.244	0.007	0.500
configureRSPA	0.026	0.006	0.062
format_mGWA	0.851	0.024	1.731
format_mQTL	1.484	0.026	2.959
load_datafiles	0.023	0.006	0.047
load_demo_data	0.001	0.000	0.001
mQTL.NMR-package	57.808	0.451	66.649
matchSegments	1.297	0.025	1.558
normalise	0.300	0.002	0.303
normalise_mQTL	3.463	0.061	4.017
peakPeaks	0.860	0.012	0.891
post_mQTL	0.392	0.034	0.525
ppersp	0.050	0.013	0.106
pplot	0.040	0.013	0.073
pre_mQTL	54.306	0.367	61.441
process_mGWA	6.098	0.036	6.188
process_mQTL	0.798	0.019	0.816
segmentateSp	1.171	0.017	1.200
selectRefSp	1.704	0.005	1.717
setupRSPA	0.024	0.006	0.030
sgolay	0.002	0.001	0.001
sgolayDeriv	0.283	0.000	0.285
simple.plot	2.266	0.030	2.312
summary_mQTL	0.033	0.010	0.044