Package: mQTL.NMR

Version: 1.12.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.12.0.tar.gz

StartedAt: 2018-04-12 01:17:46 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:19:52 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 126.1 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.12.0’
* 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 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 28.540  0.044  28.604
pre_mQTL         26.636  0.036  26.697
align_mQTL       23.224  0.028  23.290
process_mGWA      6.400  0.000   6.407
* 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-3.6-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	1.244	0.016	1.260
SRV.plot	1.392	0.008	1.399
SRV_lod.plot	0.092	0.000	0.094
Top_SRV.plot	1.236	0.012	1.247
alignSp	0.956	0.004	0.962
align_mQTL	23.224	0.028	23.290
attachSegments	0.508	0.008	0.513
circle_mQTL	0.224	0.004	0.227
configureRSPA	0.004	0.004	0.007
format_mGWA	0.684	0.000	0.684
format_mQTL	0.944	0.004	0.947
load_datafiles	0.008	0.000	0.006
load_demo_data	0.000	0.000	0.001
mQTL.NMR-package	28.540	0.044	28.604
matchSegments	0.560	0.004	0.566
normalise	0.232	0.000	0.235
normalise_mQTL	1.504	0.012	1.517
peakPeaks	0.240	0.000	0.242
post_mQTL	0.216	0.008	0.224
ppersp	0.028	0.000	0.027
pplot	0.008	0.004	0.014
pre_mQTL	26.636	0.036	26.697
process_mGWA	6.400	0.000	6.407
process_mQTL	0.592	0.000	0.596
segmentateSp	0.392	0.000	0.393
selectRefSp	0.796	0.000	0.794
setupRSPA	0.000	0.004	0.004
sgolay	0.000	0.000	0.001
sgolayDeriv	0.080	0.000	0.084
simple.plot	0.928	0.012	0.942
summary_mQTL	0.024	0.000	0.024