BioC 3.2: CHECK report for mQTL.NMR on perceval

Package: mQTL.NMR

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.3.0.tar.gz

StartedAt: 2015-08-24 03:03:02 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:07:59 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 297.8 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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.3.0’
* 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 ... [3s/5s] 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 ... [210s/239s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 61.210  1.177  76.819
pre_mQTL         58.208  0.883  69.899
align_mQTL       53.083  0.782  54.313
process_mGWA      9.710  0.067  10.753
* 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-3.2-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	2.216	0.064	2.754
SRV.plot	2.310	0.066	2.712
SRV_lod.plot	0.121	0.004	0.163
Top_SRV.plot	1.938	0.053	2.199
alignSp	1.317	0.041	1.546
align_mQTL	53.083	0.782	54.313
attachSegments	1.030	0.032	1.063
circle_mQTL	0.159	0.003	0.163
configureRSPA	0.006	0.001	0.007
format_mGWA	0.527	0.015	0.553
format_mQTL	0.982	0.036	1.020
load_datafiles	0.005	0.001	0.006
load_demo_data	0.001	0.000	0.001
mQTL.NMR-package	61.210	1.177	76.819
matchSegments	1.318	0.044	1.491
normalise	0.362	0.005	0.368
normalise_mQTL	2.947	0.119	3.284
peakPeaks	0.673	0.012	0.761
post_mQTL	0.479	0.047	0.606
ppersp	0.032	0.011	0.052
pplot	0.021	0.010	0.035
pre_mQTL	58.208	0.883	69.899
process_mGWA	9.710	0.067	10.753
process_mQTL	0.844	0.021	1.077
segmentateSp	1.303	0.028	1.538
selectRefSp	1.518	0.011	1.729
setupRSPA	0.007	0.001	0.010
sgolay	0.001	0.000	0.001
sgolayDeriv	0.331	0.018	0.403
simple.plot	2.303	0.060	2.537
summary_mQTL	0.015	0.001	0.017