BioC 3.2: CHECK report for mQTL.NMR on perceval

Package: mQTL.NMR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.4.0.tar.gz

StartedAt: 2015-11-10 07:22:15 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 07:26:36 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 261.2 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 mQTL.NMR_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.4.0’
* 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 ... 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 ... [190s/202s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
align_mQTL       59.354  0.737  71.015
mQTL.NMR-package 51.497  0.667  52.583
pre_mQTL         49.030  0.611  49.682
process_mGWA      6.621  0.040   6.662
* 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
  ‘/Users/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	1.706	0.032	1.736
SRV.plot	1.844	0.038	1.882
SRV_lod.plot	0.138	0.003	0.141
Top_SRV.plot	1.657	0.030	1.688
alignSp	1.133	0.024	1.158
align_mQTL	59.354	0.737	71.015
attachSegments	0.897	0.027	0.923
circle_mQTL	0.163	0.003	0.166
configureRSPA	0.007	0.001	0.007
format_mGWA	0.477	0.011	0.488
format_mQTL	1.032	0.031	1.062
load_datafiles	0.005	0.000	0.006
load_demo_data	0.000	0.000	0.001
mQTL.NMR-package	51.497	0.667	52.583
matchSegments	1.144	0.024	1.168
normalise	0.265	0.003	0.268
normalise_mQTL	2.866	0.087	2.972
peakPeaks	0.540	0.007	0.548
post_mQTL	0.442	0.033	0.507
ppersp	0.029	0.008	0.038
pplot	0.018	0.007	0.026
pre_mQTL	49.030	0.611	49.682
process_mGWA	6.621	0.040	6.662
process_mQTL	0.860	0.018	0.878
segmentateSp	1.041	0.026	1.067
selectRefSp	1.366	0.015	1.382
setupRSPA	0.006	0.001	0.007
sgolay	0.001	0.000	0.001
sgolayDeriv	0.237	0.001	0.238
simple.plot	1.903	0.032	1.935
summary_mQTL	0.028	0.002	0.030