BioC 3.3: CHECK report for mQTL.NMR on morelia

Package: mQTL.NMR

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.5.0.tar.gz

StartedAt: 2015-10-22 08:46:19 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 08:48:57 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 157.6 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_1.5.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/mQTL.NMR.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.5.0’
* 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 ... [127s/127s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 37.050  0.387  37.550
pre_mQTL         35.382  0.386  35.794
align_mQTL       29.863  0.286  30.191
* 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
  ‘/Users/biocbuild/bbs-3.3-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	2.112	0.038	2.153
SRV.plot	1.941	0.027	1.969
SRV_lod.plot	0.112	0.002	0.115
Top_SRV.plot	1.655	0.019	1.683
alignSp	0.918	0.009	0.927
align_mQTL	29.863	0.286	30.191
attachSegments	0.90	0.02	0.92
circle_mQTL	0.164	0.001	0.166
configureRSPA	0.004	0.001	0.004
format_mGWA	0.497	0.008	0.520
format_mQTL	0.972	0.016	0.998
load_datafiles	0.003	0.000	0.004
load_demo_data	0.001	0.000	0.000
mQTL.NMR-package	37.050	0.387	37.550
matchSegments	0.689	0.008	0.696
normalise	0.167	0.001	0.168
normalise_mQTL	2.096	0.043	2.142
peakPeaks	0.469	0.004	0.474
post_mQTL	0.282	0.024	0.351
ppersp	0.021	0.007	0.029
pplot	0.013	0.005	0.019
pre_mQTL	35.382	0.386	35.794
process_mGWA	4.495	0.025	4.535
process_mQTL	0.702	0.011	0.717
segmentateSp	0.776	0.012	0.788
selectRefSp	1.402	0.006	1.409
setupRSPA	0.006	0.001	0.006
sgolay	0.002	0.000	0.001
sgolayDeriv	0.122	0.000	0.122
simple.plot	1.417	0.023	1.440
summary_mQTL	0.018	0.001	0.020