BioC 3.1: CHECK report for mQTL.NMR on petty

Package: mQTL.NMR

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.2.0.tar.gz

StartedAt: 2015-10-09 00:30:09 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 00:40:31 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 622.3 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_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* 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 ‘1.2.0’
* 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 ... [4s/4s] 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 ... [213s/566s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
align_mQTL       67.458  0.754  95.084
mQTL.NMR-package 62.394  1.299 193.507
pre_mQTL         50.375  0.780 152.760
process_mGWA      6.228  0.061  18.582
normalise_mQTL    2.991  0.135  26.029
simple.plot       1.959  0.042   8.993
matchSegments     1.115  0.052  14.974
segmentateSp      1.082  0.051   8.098
format_mQTL       0.905  0.045   8.654
format_mGWA       0.500  0.044  17.528
* 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-3.1-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	2.217	0.040	2.256
SRV.plot	2.470	0.049	2.520
SRV_lod.plot	0.128	0.003	0.131
Top_SRV.plot	2.245	0.041	2.288
alignSp	1.519	0.030	1.551
align_mQTL	67.458	0.754	95.084
attachSegments	0.878	0.032	1.055
circle_mQTL	0.163	0.002	0.486
configureRSPA	0.006	0.001	0.007
format_mGWA	0.500	0.044	17.528
format_mQTL	0.905	0.045	8.654
load_datafiles	0.005	0.001	0.006
load_demo_data	0.001	0.000	0.000
mQTL.NMR-package	62.394	1.299	193.507
matchSegments	1.115	0.052	14.974
normalise	0.271	0.011	0.282
normalise_mQTL	2.991	0.135	26.029
peakPeaks	0.577	0.010	1.414
post_mQTL	0.397	0.045	2.479
ppersp	0.027	0.007	0.034
pplot	0.017	0.006	0.039
pre_mQTL	50.375	0.780	152.760
process_mGWA	6.228	0.061	18.582
process_mQTL	0.860	0.023	1.016
segmentateSp	1.082	0.051	8.098
selectRefSp	1.317	0.014	1.331
setupRSPA	0.006	0.001	0.085
sgolay	0.001	0.000	0.001
sgolayDeriv	0.240	0.001	0.259
simple.plot	1.959	0.042	8.993
summary_mQTL	0.026	0.002	0.103