Multiple platform build/check report for BioC 3.7 - CHECK report for mQTL.NMR on merida2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mQTL.NMR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mQTL.NMR_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.5.0 (2018-04-23)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 58.545  0.353  59.255
pre_mQTL         58.548  0.257  59.234
align_mQTL       51.663  0.318  52.320
process_mGWA      7.053  0.026   7.129
* 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-3.7-bioc/meat/mQTL.NMR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mQTL.NMR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘mQTL.NMR’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mQTL.NMR)

Tests output

Example timings

name	user	system	elapsed
SRV	2.133	0.043	2.185
SRV.plot	1.836	0.045	1.895
SRV_lod.plot	0.135	0.002	0.143
Top_SRV.plot	1.617	0.026	1.654
alignSp	1.030	0.024	1.058
align_mQTL	51.663	0.318	52.320
attachSegments	0.714	0.010	0.728
circle_mQTL	0.143	0.001	0.146
configureRSPA	0.008	0.001	0.009
format_mGWA	0.578	0.013	0.603
format_mQTL	0.897	0.015	0.920
load_datafiles	0.005	0.001	0.005
load_demo_data	0.001	0.000	0.001
mQTL.NMR-package	58.545	0.353	59.255
matchSegments	0.818	0.013	0.837
normalise	0.507	0.007	0.520
normalise_mQTL	2.487	0.051	2.565
peakPeaks	0.330	0.004	0.334
post_mQTL	0.429	0.041	0.484
ppersp	0.032	0.007	0.039
pplot	0.023	0.009	0.031
pre_mQTL	58.548	0.257	59.234
process_mGWA	7.053	0.026	7.129
process_mQTL	0.743	0.018	0.767
segmentateSp	0.737	0.014	0.755
selectRefSp	1.841	0.005	1.856
setupRSPA	0.008	0.001	0.009
sgolay	0.002	0.000	0.001
sgolayDeriv	0.145	0.001	0.147
simple.plot	1.546	0.025	1.586
summary_mQTL	0.020	0.002	0.022

CHECK report for mQTL.NMR on merida2

Summary

Command output

Installation output

Tests output

Example timings