BioC 3.5: CHECK report for mQTL.NMR on toluca2

Package: mQTL.NMR

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.9.0.tar.gz

StartedAt: 2017-04-23 07:01:57 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 07:05:58 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 240.8 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/mQTL.NMR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.9.0’
* 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 52.778  0.379  61.529
pre_mQTL         44.406  0.310  45.950
align_mQTL       43.558  0.272  56.076
process_mGWA      6.513  0.032   6.606
* 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-3.5-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	2.394	0.041	3.472
SRV.plot	2.463	0.035	3.070
SRV_lod.plot	0.834	0.005	1.087
Top_SRV.plot	2.347	0.032	2.629
alignSp	2.028	0.012	2.867
align_mQTL	43.558	0.272	56.076
attachSegments	1.123	0.022	1.713
circle_mQTL	0.227	0.003	0.338
configureRSPA	0.006	0.001	0.007
format_mGWA	0.745	0.016	0.875
format_mQTL	1.251	0.018	1.625
load_datafiles	0.005	0.000	0.011
load_demo_data	0	0	0
mQTL.NMR-package	52.778	0.379	61.529
matchSegments	0.994	0.017	1.020
normalise	0.370	0.002	0.377
normalise_mQTL	2.777	0.060	2.973
peakPeaks	0.625	0.005	0.635
post_mQTL	0.443	0.025	0.483
ppersp	0.027	0.006	0.034
pplot	0.019	0.006	0.025
pre_mQTL	44.406	0.310	45.950
process_mGWA	6.513	0.032	6.606
process_mQTL	2.484	0.017	2.535
segmentateSp	0.835	0.013	0.849
selectRefSp	1.287	0.004	1.292
setupRSPA	0.005	0.001	0.006
sgolay	0.001	0.000	0.001
sgolayDeriv	0.159	0.000	0.160
simple.plot	1.925	0.021	1.958
summary_mQTL	0.013	0.001	0.014