BioC 3.2: CHECK report for mQTL.NMR on zin1

Package: mQTL.NMR

Version: 1.3.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.3.0.tar.gz

StartedAt: 2015-08-24 01:57:38 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 02:00:21 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 163.3 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.3.0’
* 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 ... NOTE
Found the following CITATION file in a non-standard place:
  inst/CITATION.Rd
Most likely ‘inst/CITATION’ should be used instead.
* 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 ... [131s/134s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 39.816  0.052  39.985
align_mQTL       35.892  0.024  38.188
pre_mQTL         35.682  0.060  35.860
* 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

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck/00check.log’
for details.

* 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	1.357	0.004	1.387
SRV.plot	1.604	0.012	1.988
SRV_lod.plot	0.085	0.000	0.085
Top_SRV.plot	1.369	0.016	1.389
alignSp	0.816	0.012	0.912
align_mQTL	35.892	0.024	38.188
attachSegments	0.629	0.004	0.633
circle_mQTL	0.142	0.000	0.142
configureRSPA	0.006	0.000	0.006
format_mGWA	0.549	0.000	0.577
format_mQTL	0.822	0.020	0.843
load_datafiles	0.005	0.000	0.005
load_demo_data	0.001	0.000	0.000
mQTL.NMR-package	39.816	0.052	39.985
matchSegments	0.562	0.004	0.566
normalise	0.198	0.000	0.199
normalise_mQTL	1.946	0.028	1.974
peakPeaks	0.325	0.008	0.334
post_mQTL	0.202	0.000	0.202
ppersp	0.034	0.000	0.034
pplot	0.016	0.000	0.017
pre_mQTL	35.682	0.060	35.860
process_mGWA	4.551	0.008	4.582
process_mQTL	0.786	0.000	0.786
segmentateSp	0.519	0.000	0.518
selectRefSp	0.964	0.000	0.963
setupRSPA	0.001	0.004	0.005
sgolay	0.001	0.000	0.001
sgolayDeriv	0.218	0.000	0.219
simple.plot	1.134	0.004	1.138
summary_mQTL	0.011	0.000	0.012