Multiple platform build/check report for BioC 3.8 - CHECK report for mQTL.NMR on merida1

##############################################################################
##############################################################################
###
### Running command:
###
###   /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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-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 ‘1.15.0’
* 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 57.555  0.349  58.285
pre_mQTL         57.542  0.252  58.211
align_mQTL       50.832  0.322  51.487
process_mGWA      6.999  0.031   7.077
* 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-3.8-bioc/meat/mQTL.NMR.Rcheck/00check.log’
for details.

Installation output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mQTL.NMR
###
##############################################################################
##############################################################################


* 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	2.114	0.043	2.167
SRV.plot	1.898	0.049	1.957
SRV_lod.plot	0.137	0.002	0.140
Top_SRV.plot	1.572	0.032	1.611
alignSp	1.033	0.032	1.073
align_mQTL	50.832	0.322	51.487
attachSegments	0.727	0.007	0.738
circle_mQTL	0.123	0.001	0.126
configureRSPA	0.008	0.001	0.010
format_mGWA	0.583	0.014	0.605
format_mQTL	0.886	0.017	0.907
load_datafiles	0.005	0.001	0.006
load_demo_data	0.002	0.000	0.001
mQTL.NMR-package	57.555	0.349	58.285
matchSegments	0.789	0.015	0.811
normalise	0.470	0.003	0.477
normalise_mQTL	2.361	0.079	2.455
peakPeaks	0.357	0.007	0.370
post_mQTL	0.348	0.044	0.402
ppersp	0.022	0.006	0.029
pplot	0.015	0.005	0.019
pre_mQTL	57.542	0.252	58.211
process_mGWA	6.999	0.031	7.077
process_mQTL	0.722	0.016	0.743
segmentateSp	0.801	0.015	0.819
selectRefSp	1.802	0.004	1.812
setupRSPA	0.006	0.001	0.007
sgolay	0.002	0.000	0.002
sgolayDeriv	0.134	0.000	0.133
simple.plot	1.511	0.023	1.542
summary_mQTL	0.021	0.002	0.026

CHECK report for mQTL.NMR on merida1

Summary

Command output

Installation output

Tests output

Example timings