BioC 3.4: CHECK report for mQTL.NMR on morelia

Package: mQTL.NMR

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.7.0.tar.gz

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

EndedAt: 2016-09-20 09:38:39 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 150.6 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_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.7.0’
* 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 35.861  0.346  36.271
pre_mQTL         33.644  0.328  34.714
align_mQTL       30.336  0.330  30.678
* 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-3.4-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	1.260	0.019	1.279
SRV.plot	2.259	0.034	2.294
SRV_lod.plot	0.087	0.001	0.090
Top_SRV.plot	1.812	0.026	1.840
alignSp	0.816	0.018	0.834
align_mQTL	30.336	0.330	30.678
attachSegments	0.755	0.011	0.767
circle_mQTL	0.161	0.002	0.163
configureRSPA	0.007	0.001	0.008
format_mGWA	0.501	0.008	0.542
format_mQTL	0.792	0.015	0.807
load_datafiles	0.003	0.000	0.004
load_demo_data	0.001	0.000	0.000
mQTL.NMR-package	35.861	0.346	36.271
matchSegments	0.920	0.016	0.936
normalise	0.228	0.002	0.232
normalise_mQTL	2.104	0.053	2.223
peakPeaks	0.451	0.005	0.456
post_mQTL	0.273	0.026	0.306
ppersp	0.030	0.006	0.036
pplot	0.019	0.006	0.025
pre_mQTL	33.644	0.328	34.714
process_mGWA	3.903	0.020	3.941
process_mQTL	0.473	0.012	0.485
segmentateSp	0.742	0.016	0.758
selectRefSp	0.987	0.003	0.991
setupRSPA	0.005	0.000	0.005
sgolay	0.001	0.000	0.001
sgolayDeriv	0.13	0.00	0.13
simple.plot	1.591	0.020	1.612
summary_mQTL	0.011	0.001	0.011