BioC 3.4: CHECK report for mQTL.NMR on morelia

Package: mQTL.NMR

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.8.0.tar.gz

StartedAt: 2017-04-15 05:21:20 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 05:24:39 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 198.4 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_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.8.0’
* 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 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 45.725  0.374  46.368
pre_mQTL         44.018  0.294  44.489
align_mQTL       37.962  0.290  38.308
* 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	1.773	0.034	1.809
SRV.plot	2.413	0.036	2.453
SRV_lod.plot	0.108	0.001	0.110
Top_SRV.plot	2.217	0.024	2.241
alignSp	1.127	0.016	1.143
align_mQTL	37.962	0.290	38.308
attachSegments	0.939	0.010	0.949
circle_mQTL	0.140	0.002	0.148
configureRSPA	0.006	0.001	0.006
format_mGWA	0.640	0.013	0.691
format_mQTL	1.280	0.018	1.302
load_datafiles	0.005	0.001	0.004
load_demo_data	0.001	0.000	0.001
mQTL.NMR-package	45.725	0.374	46.368
matchSegments	0.966	0.012	0.978
normalise	0.300	0.002	0.302
normalise_mQTL	2.612	0.062	2.675
peakPeaks	0.586	0.005	0.591
post_mQTL	0.330	0.027	0.674
ppersp	0.022	0.006	0.028
pplot	0.030	0.006	0.037
pre_mQTL	44.018	0.294	44.489
process_mGWA	4.668	0.023	4.723
process_mQTL	0.504	0.012	0.515
segmentateSp	0.754	0.010	0.764
selectRefSp	0.994	0.006	1.001
setupRSPA	0.006	0.001	0.006
sgolay	0.002	0.000	0.001
sgolayDeriv	0.130	0.001	0.130
simple.plot	1.537	0.022	1.561
summary_mQTL	0.017	0.001	0.019