BioC 3.2: CHECK report for mQTL.NMR on oaxaca

Package: mQTL.NMR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mQTL.NMR_1.4.0.tar.gz

StartedAt: 2016-04-23 02:26:39 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 02:30:44 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 245.9 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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/mQTL.NMR.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.4.0’
* 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/3s] 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 ... [184s/194s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
mQTL.NMR-package 53.950  0.389  55.760
pre_mQTL         49.530  0.337  49.946
align_mQTL       48.663  0.286  51.776
process_mGWA      5.536  0.036   5.616
* 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	2.303	0.036	4.653
SRV.plot	2.887	0.048	4.809
SRV_lod.plot	0.133	0.002	0.168
Top_SRV.plot	2.617	0.039	3.219
alignSp	1.474	0.012	1.741
align_mQTL	48.663	0.286	51.776
attachSegments	1.040	0.012	1.051
circle_mQTL	0.180	0.002	0.182
configureRSPA	0.007	0.001	0.008
format_mGWA	0.761	0.014	0.816
format_mQTL	1.345	0.021	1.376
load_datafiles	0.004	0.000	0.005
load_demo_data	0.001	0.001	0.000
mQTL.NMR-package	53.950	0.389	55.760
matchSegments	1.132	0.014	1.147
normalise	0.294	0.002	0.297
normalise_mQTL	2.776	0.055	2.832
peakPeaks	0.654	0.006	0.661
post_mQTL	0.381	0.028	0.418
ppersp	0.029	0.007	0.036
pplot	0.018	0.007	0.024
pre_mQTL	49.530	0.337	49.946
process_mGWA	5.536	0.036	5.616
process_mQTL	0.737	0.013	0.751
segmentateSp	1.110	0.017	1.128
selectRefSp	1.341	0.006	1.347
setupRSPA	0.007	0.001	0.007
sgolay	0.002	0.000	0.001
sgolayDeriv	0.182	0.000	0.183
simple.plot	2.136	0.024	2.161
summary_mQTL	0.015	0.001	0.017