BioC 3.4: CHECK report for mQTL.NMR on malbec1

Package: mQTL.NMR

Version: 1.8.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.8.0.tar.gz

StartedAt: 2017-04-14 23:59:42 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-15 00:02:05 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 143.1 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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 33.988  0.052  34.084
pre_mQTL         33.196  0.024  33.253
align_mQTL       28.424  0.040  28.490
process_mGWA      5.336  0.008   5.351
* 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-3.4-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	1.292	0.012	1.308
SRV.plot	1.548	0.008	1.556
SRV_lod.plot	0.084	0.004	0.090
Top_SRV.plot	1.236	0.004	1.241
alignSp	0.672	0.008	0.679
align_mQTL	28.424	0.040	28.490
attachSegments	0.708	0.012	0.720
circle_mQTL	0.124	0.004	0.128
configureRSPA	0.004	0.000	0.005
format_mGWA	0.424	0.004	0.427
format_mQTL	0.7	0.0	0.7
load_datafiles	0.004	0.000	0.003
load_demo_data	0.000	0.004	0.001
mQTL.NMR-package	33.988	0.052	34.084
matchSegments	0.644	0.004	0.653
normalise	0.184	0.000	0.186
normalise_mQTL	1.908	0.004	1.917
peakPeaks	0.228	0.008	0.240
post_mQTL	0.172	0.000	0.175
ppersp	0.024	0.000	0.027
pplot	0.016	0.000	0.013
pre_mQTL	33.196	0.024	33.253
process_mGWA	5.336	0.008	5.351
process_mQTL	0.564	0.000	0.563
segmentateSp	0.484	0.000	0.486
selectRefSp	0.732	0.000	0.732
setupRSPA	0.004	0.004	0.008
sgolay	0.004	0.000	0.001
sgolayDeriv	0.164	0.000	0.164
simple.plot	1.212	0.012	1.224
summary_mQTL	0.020	0.000	0.019