BioC 3.2: CHECK report for mQTL.NMR on zin1

Package: mQTL.NMR

Version: 1.4.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.4.0.tar.gz

StartedAt: 2016-04-23 03:12:27 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:15:04 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 157.2 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* 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 ‘1.4.0’
* 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 ... [2s/2s] 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 ... OK
* 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 ... [130s/130s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 38.775  0.032  38.856
pre_mQTL         36.022  0.036  36.132
align_mQTL       35.650  0.027  35.793
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.2-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	1.334	0.004	1.338
SRV.plot	1.572	0.020	1.602
SRV_lod.plot	0.089	0.000	0.089
Top_SRV.plot	1.422	0.008	1.430
alignSp	0.786	0.004	0.800
align_mQTL	35.650	0.027	35.793
attachSegments	0.570	0.004	0.575
circle_mQTL	0.14	0.00	0.14
configureRSPA	0.006	0.000	0.006
format_mGWA	0.533	0.004	0.555
format_mQTL	0.786	0.008	0.809
load_datafiles	0.005	0.000	0.005
load_demo_data	0	0	0
mQTL.NMR-package	38.775	0.032	38.856
matchSegments	0.605	0.000	0.606
normalise	0.181	0.000	0.182
normalise_mQTL	1.967	0.012	1.978
peakPeaks	0.355	0.004	0.372
post_mQTL	0.205	0.008	0.212
ppersp	0.032	0.004	0.035
pplot	0.016	0.000	0.016
pre_mQTL	36.022	0.036	36.132
process_mGWA	4.423	0.000	4.426
process_mQTL	0.782	0.000	0.782
segmentateSp	0.525	0.000	0.525
selectRefSp	0.995	0.000	0.995
setupRSPA	0.005	0.000	0.005
sgolay	0.001	0.000	0.001
sgolayDeriv	0.183	0.000	0.183
simple.plot	1.212	0.004	1.214
summary_mQTL	0.012	0.000	0.012