BioC 3.2: CHECK report for mQTL.NMR on linux1.bioconductor.org

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: 2015-10-27 06:03:14 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 06:05:52 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 157.9 seconds

RetCode: 0

Status:  OK

CheckDir: mQTL.NMR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [132s/132s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 40.364  0.068  40.523
align_mQTL       37.042  0.067  37.132
pre_mQTL         34.928  0.052  35.061
process_mGWA      5.354  0.008   5.373
* 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	1.083	0.024	1.107
SRV.plot	1.455	0.012	1.467
SRV_lod.plot	0.126	0.000	0.127
Top_SRV.plot	1.817	0.008	1.826
alignSp	0.842	0.000	0.842
align_mQTL	37.042	0.067	37.132
attachSegments	0.721	0.000	0.720
circle_mQTL	0.14	0.00	0.14
configureRSPA	0.004	0.000	0.004
format_mGWA	0.380	0.008	0.391
format_mQTL	0.614	0.000	0.614
load_datafiles	0.004	0.000	0.004
load_demo_data	0	0	0
mQTL.NMR-package	40.364	0.068	40.523
matchSegments	0.491	0.004	0.496
normalise	0.158	0.000	0.158
normalise_mQTL	1.525	0.004	1.529
peakPeaks	0.286	0.000	0.287
post_mQTL	0.273	0.004	0.278
ppersp	0.044	0.000	0.045
pplot	0.016	0.004	0.020
pre_mQTL	34.928	0.052	35.061
process_mGWA	5.354	0.008	5.373
process_mQTL	0.622	0.000	0.622
segmentateSp	0.464	0.000	0.465
selectRefSp	0.897	0.000	0.899
setupRSPA	0.004	0.000	0.004
sgolay	0.001	0.000	0.001
sgolayDeriv	0.132	0.000	0.132
simple.plot	0.938	0.004	0.943
summary_mQTL	0.01	0.00	0.01