BioC 3.3: CHECK report for mQTL.NMR on oaxaca

Package: mQTL.NMR

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.6.0.tar.gz

StartedAt: 2016-10-13 03:54:38 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 03:58:28 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 229.5 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_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.6.0’
* 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 ... 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 ... NOTE
circle_mQTL: no visible global function definition for ‘rainbow’
post_mQTL: no visible global function definition for ‘dev.new’
post_mQTL: no visible global function definition for ‘png’
post_mQTL: no visible global function definition for ‘dev.off’
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette dev.new dev.off png rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "png", "rainbow")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 55.386  0.369  64.201
pre_mQTL         47.572  0.358  48.283
align_mQTL       44.948  0.333  45.572
process_mGWA      5.025  0.030   5.164
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-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	2.048	0.039	2.103
SRV.plot	2.592	0.036	2.854
SRV_lod.plot	0.123	0.002	0.188
Top_SRV.plot	2.284	0.028	2.315
alignSp	1.256	0.016	1.272
align_mQTL	44.948	0.333	45.572
attachSegments	1.112	0.011	1.126
circle_mQTL	0.156	0.001	0.184
configureRSPA	0.005	0.000	0.007
format_mGWA	0.638	0.013	0.741
format_mQTL	1.011	0.020	1.032
load_datafiles	0.006	0.000	0.006
load_demo_data	0.001	0.000	0.001
mQTL.NMR-package	55.386	0.369	64.201
matchSegments	1.260	0.013	1.523
normalise	0.324	0.002	0.469
normalise_mQTL	3.040	0.078	3.674
peakPeaks	0.643	0.007	0.707
post_mQTL	0.377	0.028	0.528
ppersp	0.031	0.008	0.051
pplot	0.020	0.007	0.035
pre_mQTL	47.572	0.358	48.283
process_mGWA	5.025	0.030	5.164
process_mQTL	0.628	0.012	0.639
segmentateSp	0.972	0.015	0.987
selectRefSp	1.185	0.003	1.189
setupRSPA	0.004	0.001	0.004
sgolay	0.001	0.000	0.001
sgolayDeriv	0.180	0.000	0.179
simple.plot	1.977	0.024	2.042
summary_mQTL	0.016	0.001	0.016