BioC 3.5: CHECK report for mQTL.NMR on malbec2

Package: mQTL.NMR

Version: 1.10.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.10.0.tar.gz

StartedAt: 2017-10-18 00:59:49 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:02:01 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 132.7 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.10.0’
* 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 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 31.960  0.056  32.045
pre_mQTL         26.004  0.040  26.085
align_mQTL       24.924  0.012  24.963
process_mGWA      6.236  0.000   6.241
* 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
  ‘/home/biocbuild/bbs-3.5-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	1.224	0.012	1.237
SRV.plot	1.264	0.004	1.267
SRV_lod.plot	0.620	0.000	0.621
Top_SRV.plot	1.392	0.004	1.395
alignSp	1.100	0.004	1.106
align_mQTL	24.924	0.012	24.963
attachSegments	0.612	0.004	0.613
circle_mQTL	0.144	0.000	0.145
configureRSPA	0.004	0.000	0.005
format_mGWA	0.592	0.008	0.600
format_mQTL	0.872	0.004	0.877
load_datafiles	0.004	0.000	0.004
load_demo_data	0	0	0
mQTL.NMR-package	31.960	0.056	32.045
matchSegments	0.476	0.000	0.476
normalise	0.264	0.000	0.263
normalise_mQTL	1.892	0.008	1.900
peakPeaks	0.252	0.000	0.255
post_mQTL	0.276	0.004	0.283
ppersp	0.024	0.004	0.026
pplot	0.012	0.000	0.013
pre_mQTL	26.004	0.040	26.085
process_mGWA	6.236	0.000	6.241
process_mQTL	1.812	0.000	1.813
segmentateSp	0.424	0.000	0.427
selectRefSp	0.904	0.000	0.906
setupRSPA	0.004	0.000	0.005
sgolay	0	0	0
sgolayDeriv	0.088	0.000	0.087
simple.plot	1.004	0.012	1.017
summary_mQTL	0.012	0.000	0.010