BioC 3.4: CHECK report for mQTL.NMR on zin1

Package: mQTL.NMR

Version: 1.7.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.7.0.tar.gz

StartedAt: 2016-09-20 09:36:47 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 09:39:03 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 136.0 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_1.7.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.7.0’
* 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 34.004  0.056  34.150
pre_mQTL         30.368  0.012  30.644
align_mQTL       29.852  0.032  29.885
* 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	1.112	0.012	1.126
SRV.plot	1.324	0.012	1.338
SRV_lod.plot	0.088	0.000	0.088
Top_SRV.plot	1.188	0.016	1.203
alignSp	0.680	0.000	0.678
align_mQTL	29.852	0.032	29.885
attachSegments	0.536	0.004	0.539
circle_mQTL	0.120	0.000	0.119
configureRSPA	0.004	0.000	0.004
format_mGWA	0.428	0.004	0.444
format_mQTL	0.668	0.000	0.670
load_datafiles	0.004	0.000	0.004
load_demo_data	0.000	0.000	0.001
mQTL.NMR-package	34.004	0.056	34.150
matchSegments	0.524	0.004	0.526
normalise	0.196	0.000	0.192
normalise_mQTL	1.592	0.012	1.625
peakPeaks	0.244	0.004	0.248
post_mQTL	0.192	0.000	0.191
ppersp	0.024	0.000	0.027
pplot	0.012	0.000	0.014
pre_mQTL	30.368	0.012	30.644
process_mGWA	4.132	0.004	4.138
process_mQTL	1.144	0.000	1.142
segmentateSp	0.468	0.000	0.468
selectRefSp	0.956	0.000	0.955
setupRSPA	0.004	0.000	0.005
sgolay	0	0	0
sgolayDeriv	0.216	0.000	0.219
simple.plot	0.952	0.004	0.959
summary_mQTL	0.008	0.000	0.011