Package: mQTL.NMR

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.12.0.tar.gz

StartedAt: 2018-04-12 06:45:52 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 06:48:43 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 170.5 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 37.183  0.260  38.483
pre_mQTL         34.307  0.222  35.634
align_mQTL       32.080  0.182  32.832
process_mGWA      6.147  0.032   6.369
* 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-3.6-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	1.654	0.034	1.713
SRV.plot	1.797	0.040	1.856
SRV_lod.plot	0.107	0.002	0.115
Top_SRV.plot	1.716	0.020	1.761
alignSp	1.273	0.010	1.300
align_mQTL	32.080	0.182	32.832
attachSegments	0.771	0.007	0.795
circle_mQTL	0.167	0.001	0.171
configureRSPA	0.005	0.001	0.006
format_mGWA	0.572	0.014	0.612
format_mQTL	0.911	0.013	0.957
load_datafiles	0.005	0.000	0.005
load_demo_data	0.001	0.001	0.001
mQTL.NMR-package	37.183	0.260	38.483
matchSegments	0.793	0.008	0.826
normalise	0.359	0.004	0.372
normalise_mQTL	2.277	0.046	2.434
peakPeaks	0.417	0.003	0.434
post_mQTL	0.399	0.024	0.440
ppersp	0.026	0.007	0.035
pplot	0.018	0.006	0.024
pre_mQTL	34.307	0.222	35.634
process_mGWA	6.147	0.032	6.369
process_mQTL	0.602	0.014	0.652
segmentateSp	0.630	0.011	0.660
selectRefSp	1.116	0.005	1.137
setupRSPA	0.005	0.001	0.006
sgolay	0.002	0.000	0.001
sgolayDeriv	0.117	0.001	0.118
simple.plot	1.478	0.021	1.577
summary_mQTL	0.014	0.001	0.016