Package: mQTL.NMR

Version: 1.15.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mQTL.NMR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mQTL.NMR_1.15.0.tar.gz

StartedAt: 2018-06-25 02:04:03 -0400 (Mon, 25 Jun 2018)

EndedAt: 2018-06-25 02:06:23 -0400 (Mon, 25 Jun 2018)

EllapsedTime: 139.2 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:mQTL.NMR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings mQTL.NMR_1.15.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.5.0 Patched (2018-05-03 r74699)
* 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 ‘1.15.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 33.932  0.048  34.008
pre_mQTL         32.460  0.020  32.507
align_mQTL       30.020  0.032  30.074
process_mGWA      6.260  0.012   6.293
* 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-3.8-bioc/meat/mQTL.NMR.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL mQTL.NMR
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘mQTL.NMR’ ...
** R
** inst
** byte-compile and prepare 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	1.356	0.008	1.372
SRV.plot	1.276	0.016	1.304
SRV_lod.plot	0.084	0.000	0.096
Top_SRV.plot	1.156	0.020	1.179
alignSp	0.644	0.020	0.662
align_mQTL	30.020	0.032	30.074
attachSegments	0.448	0.004	0.449
circle_mQTL	0.100	0.000	0.101
configureRSPA	0.004	0.000	0.004
format_mGWA	0.552	0.004	0.698
format_mQTL	0.724	0.004	0.729
load_datafiles	0.004	0.000	0.003
load_demo_data	0.000	0.000	0.001
mQTL.NMR-package	33.932	0.048	34.008
matchSegments	0.524	0.000	0.523
normalise	0.312	0.000	0.310
normalise_mQTL	1.420	0.016	1.435
peakPeaks	0.176	0.004	0.182
post_mQTL	0.152	0.004	0.153
ppersp	0.024	0.004	0.029
pplot	0.012	0.000	0.012
pre_mQTL	32.460	0.020	32.507
process_mGWA	6.260	0.012	6.293
process_mQTL	0.528	0.000	0.530
segmentateSp	0.396	0.000	0.399
selectRefSp	1.084	0.000	1.088
setupRSPA	0.004	0.000	0.004
sgolay	0.000	0.000	0.001
sgolayDeriv	0.088	0.000	0.092
simple.plot	0.912	0.008	0.922
summary_mQTL	0.012	0.000	0.011