BioC 3.1: CHECK report for mQTL.NMR on morelia

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 04:14:19 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 04:18:01 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 221.9 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.0’
* 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 ... [2s/2s] 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 ... [181s/187s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
align_mQTL       49.774  2.324  56.972
mQTL.NMR-package 48.675  2.072  50.961
pre_mQTL         46.913  2.131  49.114
process_mGWA      5.287  0.378   5.684
* 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	1.869	0.067	1.937
SRV.plot	2.431	0.081	2.514
SRV_lod.plot	0.115	0.002	0.119
Top_SRV.plot	2.261	0.136	2.534
alignSp	1.426	0.074	1.666
align_mQTL	49.774	2.324	56.972
attachSegments	0.978	0.090	1.076
circle_mQTL	0.114	0.002	0.116
configureRSPA	0.004	0.000	0.004
format_mGWA	0.706	0.020	0.744
format_mQTL	1.353	0.032	1.386
load_datafiles	0.005	0.001	0.005
load_demo_data	0.001	0.000	0.001
mQTL.NMR-package	48.675	2.072	50.961
matchSegments	0.97	0.03	1.00
normalise	0.278	0.036	0.313
normalise_mQTL	2.875	0.123	3.001
peakPeaks	0.733	0.058	0.791
post_mQTL	0.349	0.036	0.392
ppersp	0.026	0.015	0.041
pplot	0.016	0.015	0.031
pre_mQTL	46.913	2.131	49.114
process_mGWA	5.287	0.378	5.684
process_mQTL	0.620	0.037	0.657
segmentateSp	0.976	0.047	1.026
selectRefSp	1.401	0.045	1.447
setupRSPA	0.006	0.001	0.007
sgolay	0.001	0.000	0.001
sgolayDeriv	0.262	0.014	0.276
simple.plot	1.909	0.024	1.935
summary_mQTL	0.024	0.001	0.025